When Solo was approaching the island the film was in color, but when Solo's boat was hit by Strago's sound barrier and was exploding it was in black and white.
The nuclear missiles are actually torpedoes, the design of which is not aerodynamic enough to be an adequate missile.
As Illya is talking with a lady while missiles are moving on an over-head rack, metal wires are visible trailing from a missile. These are probably used for guiding the missile prop.